[gmx-developers] distance restraints and domain decomposition

[Berk Hess]

Hi,

The code takes PBC into account, both for intra- and intermolecular 
interactions.

Could you provide me with the input to grompp?

Cheers,

Berk

On 06/07/2018 08:37 AM, Kutzner, Carsten wrote:
>
>> On 7. Jun 2018, at 07:02, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>>
>> Den 2018-06-06 kl. 15:07, skrev Kutzner, Carsten:
>>> Dear developers,
>>> we have a ~ 40,000 atom MD system with distance restraints (bond type 6)
>>> that does not want to run in parallel, although I assume it should.
>>> It runs fine without DD, e.g. -ntmpi 1 -ntomp 20, however with DD the
>>> following happens:
>>> mdrun -ntmpi 2
>>> Fatal error:
>>> There is no domain decomposition for 2 ranks that is compatible with the given
>>> box and a minimum cell size of 11.4939 nm
>>> The maximum distance restraint distance is however at 4.0 nm, so 11.49 nm as
>>> reported cannot be true, unless the PBC distance is not taken properly
>>> into account. Is this the expected behaviour or worth generating a redmine
>>> issue?
>>> Thanks,
>>>   Carsten
>> Which version?
> 2018
>
>> It should work with OpenMP anyway.
> Yes, that works, however we might want to use multiple nodes and/or multiple
> GPUs for similar setups in the future.
>
> Carsten
>
>> -- 
>> David van der Spoel, Ph.D., Professor of Biology
>> Head of Department, Cell & Molecular Biology, Uppsala University.
>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>> http://www.icm.uu.se
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> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/grubmueller/kutzner
> http://www.mpibpc.mpg.de/grubmueller/sppexa
>